Development of dengue virus vaccine components

ABSTRACT

The invention is related to a dengue virus or chimeric dengue virus that contains a mutation in the 3′ untranslated region (3′-UTR) comprising a Δ30 mutation that removes the TL-2 homologous structure in each of the dengue virus serotypes 1, 2, 3, and 4, and nucleotides additional to the Δ30 mutation deleted from the 3′-UTR that removes sequence in the 5′ direction as far as the 5′ boundary of the TL-3 homologous structure in each of the dengue virus serotypes 1, 2, 3, and 4, or a replacement of the 3′-UTR of a dengue virus of a first serotype with the 3′-UTR of a dengue virus of a second serotype, optionally containing the Δ30 mutation and nucleotides additional to the Δ30 mutation deleted from the 3′-UTR; and immunogenic compositions, methods of inducing an immune response, and methods of producing a dengue virus or chimeric dengue virus.

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.60/837,723, filed Aug. 15, 2006, the disclosure of which is incorporatedherein by reference in its entirety.

FIELD OF THE INVENTION

The invention relates to mutations in the 3′ untranslated region of thegenome of dengue virus serotypes 1, 2, 3, and 4 that are useful inattenuating the growth characteristics of dengue virus vaccines.

DESCRIPTION OF THE RELATED ART

There are four serotypes of dengue virus (dengue virus type I [DEN1],DEN2, DEN3, and DEN4) that annually cause an estimated 50 to 100 millioncases of dengue fever and 500,000 cases of the more severe form ofdengue virus infection known as dengue hemorrhagic fever/dengue shocksyndrome (Gubler, D. J. and M. Meltzer 1999 Adv Virus Res 53:35-70).Dengue virus is widely distributed throughout the tropical andsemitropical regions of the world, and the number of dengue virusinfections continues to increase due to the expanding range of its Aedesaegypti mosquito vector. A vaccine is not available for the control ofdengue disease despite its importance as a reemerging disease. The goalof immunization is to protect against dengue virus disease by theinduction of a long-lived neutralizing antibody response against each ofthe four serotypes. Simultaneous protection against all four serotypesis required, since an increase in disease severity can occur in personswith preexisting antibodies to a heterotypic dengue virus. Suchimmunization can be achieved economically with a live, attenuated virusvaccine.

Dengue viruses are positive-sense RNA viruses belonging to theFlavivirus genus. The approximately 11,000-base genome contains a singleopen reading frame encoding a polyprotein which is processed byproteases of both viral and cellular origin into three structuralproteins (C, prM, and E) and at least seven nonstructural (NS) proteins.Both ends of the dengue virus genome contain an untranslated region(UTR), and the overall genome organization is5′-UTR-C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5-UTR-3′. The 3′ UTR isnearly 400 bases in length and is predicted to contain several stem-loopstructures conserved among dengue virus serotypes (Brinton, M. A. et al.1986 Virology 153:113-121, Hahn, C. S. et al. 1987 J Mol Biol 198:33-41,Proutski, V. et al. 1997 Nucleic Acids Res 25:1194-1202, Rauscher, S. etal. 1997 RNA 3:779-791, Shurtleff, A. et al. 2001 Virology 281:75-87).One such stern-loop structure, identified as TL-2 in the proposedsecondary structure of the 3′ UTR (Proutski, V. et al. 1997 NucleicAcids Res 25:1194-1202), was previously removed by deletion of 30nucleotides from the DEN4 genome (3′ nucleotides 172 to 143) (Men, R. etal. 1996 J Viral 70:3930-3937) and has subsequently been designated asthe Δ30 mutation (Durbin, A. P. et al. 2001 Am J Trop Med Hyg65:405-413). The resulting virus, rDEN4Δ30, was shown to be attenuatedin rhesus monkeys compared to parental viruses containing an intact TL-2sequence and is attenuated in humans (Durbin, A. P. et al. 2001 Am JTrop Med Hyg 65:405-413).

SUMMARY OF THE INVENTION

The invention is related to a dengue virus or chimeric dengue viruscomprising a mutation in the 3′ untranslated region (3′-UTR) selectedfrom the group consisting of:

-   -   (a) a Δ30 mutation that removes the TL-2 homologous structure in        each of the dengue virus serotypes 1, 2, 3, and 4, and        nucleotides additional to the Δ30 mutation deleted from the        3′-UTR that removes sequence in the 5′ direction as far as the        5′ boundary of the TL-3 homologous structure in each of the        dengue virus serotypes 1, 2, 3, and 4; and    -   (b) a replacement of the 3′-UTR of a dengue virus of a first        serotype with the 3′-UTR of a dengue virus of a second serotype,        optionally containing the Δ30 mutation and nucleotides        additional to the Δ30 mutation deleted from the 3′-UTR;

and immunogenic compositions, methods of inducing an immune response,and methods of producing a dengue virus or chimeric dengue virus.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Two approaches to attenuate dengue viruses. A) (a-c) Deletion ofadditional nucleotides from the 3′-UTR (DEN3 wt Sleman/78, SEQ ID NO:1). B) Replacement of the 3′-UTR of a dengue virus of a first serotypewith the 3′-UTR of a dengue virus of a second serotype.

FIGS. 2-5. Predicted secondary structure of the TL-1, TL-2 and TL-3region of the 3′-UTR of each DEN serotype. The GenBank accession numberof the sequence used for construction of each secondary structure modelis indicated. Only the last 278, 281, 276 and 281 nucleotides of DEN1,DEN2, DEN3, and DEN4, respectively, which comprise TL-1, TL-2 and TL-3,are used to avoid circularization of the structure and subsequentmisfolding of known and experimentally-verified structural elements. Themfold program contraints specific for each structure model areindicated. Nucleotides that border the principle deletions are circledand numbered, with nucleotide numbering beginning at the 3′ genome end(reverse-direction numbering system). FIG. 2—SEQ ID NO: 2; FIG. 3—SEQ IDNO: 3; FIG. 4—SEQ ID NO: 4; FIG. 5—SEQ ID NO: 5.

FIGS. 6-9. Δ30 deletion mutation depicted for each of the dengue virusserotypes DEN1, DEN2, DEN3 and DEN4. The Δ30 mutation deletes nt 174 to145 of DEN 1, nt 173 to 144 of DEN 2, nt 173 to 143 of DEN3, and nt 172to 143 of DEN4, with reverse-direction numbering system. The deletedregion is indicated by the Δ symbol. FIG. 6—SEQ ID NO: 6; FIG. 7—SEQ IDNO: 7; FIG. 8—SEQ ID NO: 8; FIG. 9—SEQ ID NO: 9.

FIGS. 10-13. Δ30/31 deletion mutation depicted for each of the denguevirus serotypes DEN1, DEN2, DEN3 and DEN4. In addition to the deletionof the nucleotides comprising the Δ30 mutation, the Δ31 mutation deletesnt 258 to 228 of DEN1, DEN2, DEN3, and DEN4, with reverse-directionnumbering system. The deleted region is indicated by the Δ symbol. FIG.10—SEQ ID NO: 10; FIG. 11—SEQ ID NO: 11; FIG. 12—SEQ ID NO: 12; FIG.13—SEQ ID NO: 13.

FIGS. 14-17. Δ86 deletion mutation depicted for each of the dengue virusserotypes DEN1, DEN2, DEN3 and DEN4. The Δ86 mutation deletes nt 228 to145 of DEN1, nt 228 to 144 of DEN 2, nt 228 to 143 of DEN3, and nt 228to 143 of DEN4, with reverse-direction numbering system. The deletedregion is indicated by the Δ symbol. FIG. 14—SEQ ID NO: 14; FIG. 15—SEQID NO: 15; FIG. 16—SEQ ID NO: 16; FIG. 17—SEQ ID NO: 17.

FIG. 18. Chimerization of rDEN3 with the rDEN4 or rDEN4Δ30 3′-UTR. A)Recombinant 3′-UTR chimeric dengue viruses were constructed by replacingthe 3′-UTR of rDEN3 with regions derived from either rDEN4 or rDEN4Δ30.The relative location of the Δ30 mutation in the 3′-UTR is indicated byan arrow. The junctions between the ORF and UTR for rDEN3 and rDEN4 areindicated as junctions 1 and 2, respectively. Intertypic junction 3 isalso indicated for the resulting chimeric viruses. B) Nucleotide andamino acid sequence of the junction regions are shown. For junction 3,nucleotide substitutions used to introduce a unique HpaI restrictionenzyme recognition site are shown in lower case. Junction 1—SEQ ID NOs:18 (nucleotide) and 19 (amino acid); Junction 2—SEQ ID NOs: 20(nucleotide) and 21 (amino acid); Junction 3—SEQ ID NOs: 22 (nucleotide)and 23 (amino acid).

FIG. 19. Replication in Vero cells and C6/36 cells. Four mutant viruseswere compared to wild type rDEN3 for replication in Vero cells and C6/36cells. 75 cm² flasks of confluent cells were infected at a multiplicityof infection of 0.01. Aliquots of 0.5 ml were removed from flasks dailyfor seven days. After addition of SPG to a concentration of 1×, sampleswere frozen on dry ice and stored at −80° C. Virus titer was determinedby plaque assay on Vero cells for all samples. The limit of detection is1.0 log₁₀PFU/ml.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT Definitions

Unless defined otherwise, technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. See, e.g., Singleton P andSainsbury D., Dictionary of Microbiology and Molecular Biology 3rd ed.,J. Wiley & Sons, Chichester, N.Y., 2001, and Fields Virology 4th ed.,Knipe D. M. and Howley P. M. eds, Lippincott Williams & Wilkins,Philadelphia 2001.

The term “about” means within 1, 2, or 3 nucleotides.

Mutant Dengue Viruses and Chimeric Dengue Viruses

A goal of the invention is to develop a set of type-specific, liveattenuated dengue vaccine components that can be formulated into a safe,effective, and economical tetravalent dengue vaccine. The Δ30 mutationattenuates DEN4 in rhesus monkeys (Men, R. et al. 1996 J Virol70:3930-3937)). The Δ30 mutation removes a homologous structure (TL-2)in each of the dengue virus serotypes 1, 2, 3, and 4 (FIGS. 2-5).However, the Δ30 mutation was found to not attenuate DEN3 in rhesusmonkeys.

An embodiment of the invention provides dengue viruses and chimericdengue viruses having one or more mutations that result in attenuation,methods of making such dengue viruses, and methods for using thesedengue viruses to prevent or treat dengue virus infection. The mutation(or mutations) in the dengue virus of the invention is present in the 3′untranslated region (3′-UTR) formed by the most downstream approximately384 nucleotides of the viral RNA, which have been shown to play a rolein determining attenuation. The viruses and methods of the invention aredescribed further, as follows.

One example of a dengue virus that can be used in the invention is theserotype 3, Sleman/78 strain. The applicability of the invention to allmembers of the dengue virus taxonomic group is inferred by theobservation that the properties of other dengue virus strains aresimilar to that of any one dengue virus strain. Dengue viruses have beengrouped into four serotypes (DEN1, DEN2, DEN3 and DEN4). Numerousstrains have been identified for each of the four serotypes. Thecomplete genomic sequences of various dengue virus strains are providedas Genbank accession numbers in Table A.

TABLE A Examples of Dengue Virus Strains Serotype Strain Accession No. 102-20 AB178040 1 16007 AF180817 1 16007 PDK-13 AF180818 1 259par00AF514883 1 280par00 AF514878 1 293arg00 AY206457 1 295arg00 AF514885 1297arg00 AF514889 1 301arg00 AF514876 1 98901518 AB189120 1 98901530AB189121 1 A88 AB074761 1 Abidjan AF298807 1 ARG0028 AY277665 1 ARG0048AY277666 1 ARG9920 AY277664 1 BR-90 AF226685 1 BR-01-MR AF513110 1BR-97-111 AF311956 1 BR-97-233 AF311958 1 BR-97-409 AF311957 1 CambodiaAF309641 1 FGA-89 AF226687 1 FGA-NA d1d AF226686 1 Fj231-04 DQ193572 1GD05-99 AY376738 1 GD23-95 AY373427 1 GZ-80 AF350498 1D1-hu-Yap-NIID27-2004 AB204803 1 D1-H-IMTSSA-98-606 AF298808 1 MochizukiAB074760 1 D1.Myanmar.059-01 AY708047 1 D1.Myanmar.194-01 AY713474 1D1.Myanmar.206-01 AY713475 1 D1.Myanmar.23819-96 AY722802 1D1.Myanmar.305-01 AY713476 1 D1.Myanmar.31459-98 AY726555 1D1.Myanmar.31987-98 AY726554 1 D1.Myanmar.32514-98 AY722803 1D1.Myanmar.37726-01 AY726549 1 D1.Myanmar.38862-01 AY726550 1D1.Myanmar.40553-71 AY713473 1 D1.Myanmar.40568-76 AY722801 1D1.Myanmar.44168-01 AY726551 1 D1.Myanmar.44988-02 AY726552 1D1.Myanmar.49440-02 AY726553 1 rWestern Pacific-delta30 AY145123 1Western Pacific rDEN1mutF AY145122 1 S275-90 A75711 1D1-hu-Seychelles-NIID41-2003 AB195673 1 Singapore 8114-93 AY762084 1Singapore S275-90 M87512 1 ThD1_0008_81 AY732483 1 ThD1_0049_01 AY7324821 ThD1_0081_82 AY732481 1 ThD1_0097_94 AY732480 1 ThD1_0102_01 AY7324791 ThD1_0323_91 AY732478 1 ThD1_0336_91 AY732477 1 ThD1_0442_80 AY7324761 ThD1_0488_94 AY732475 1 ThD1_0673_80 AY732474 1 Recombinant WesternPacific AY145121 1 Nauru Island Western Pacific 45AZ5 NC_001477 1 NauruIsland, Western Pacific Bethesda U88535 1 Nauru Island Western Pacific45AZ5-PDK27 U88537 2 131 AF100469 2 16681-PDK53 M84728 2 16681 BlokM84727 2 16681 Kinney U87411 2 43 AF204178 2 44 AF204177 2 98900663AB189122 2 98900665 AB189123 2 98900666 AB189124 2 BA05i AY858035 2Bangkok 1974 AJ487271 2 BR64022 AF489932 2 C0166 AF100463 2 C0167AF100464 2 C0371 AF100461 2 C0390 AF100462 2 China 04 AF119661 2Cuba115-97 AY702036 2 Cuba13-97 AY702034 2 Cuba165-97 AY702038 2Cuba205-97 AY702039 2 Cuba58-97 AY702035 2 Cuba89-97 AY702037 2 DR23-01AB122020 2 DR31-01 AB122021 2 DR59-01 AB122022 2 FJ-10 AF276619 2FJ11-99 AF359579 2 I348600 AY702040 2 IQT1797 AF100467 2 IQT2913AF100468 2 Jamaica-N.1409 M20558 2 K0008 AF100459 2 K0010 AF100460 2Mara4 AF100466 2 DEN2-H-IMTSSA-MART-98-703 AF208496 2 New Guinea CAF038403 2 New Guinea C-PUO-218 hybrid AF038402 2 New Guinea-C M29095 2PDK-53 U87412 2 S1 vaccine NC_001474 2 TB16i AY858036 2 ThD2_0017_98DQ181799 2 ThD2_0026_88 DQ181802 2 ThD2_0038_74 DQ181806 2 ThD2_0055_99DQ181798 2 ThD2_0078_01 DQ181797 2 ThD2_0168_79 DQ181805 2 ThD2_0263_95DQ181800 2 ThD2_0284_90 DQ181801 2 ThD2_0433_85 DQ181803 2 ThD2_0498_84DQ181804 2 ThNH-28-93 AF022435 2 ThNH29-93 AF169678 2 ThNH36-93 AF1696792 ThNH45-93 AF169680 2 ThNH-52-93 AF022436 2 ThNH54-93 AF169682 2ThNH55-93 AF169681 2 ThNH62-93 AF169683 2 ThNH63-93 AF169684 2 ThNH69-93AF169685 2 ThNH73-93 AF169686 2 ThNH76-93 AF169687 2 ThNH81-93 AF1696882 ThNH-p36-93 AF022441 2 ThNH-7-93 AF022434 2 ThNH-p11-93 AF022437 2ThNH-p12-93 AF022438 2 ThNH-p14-93 AF022439 2 ThNH-p16-93 AF022440 2Tonga-74 AY744147 2 TSV01 AY037116 2 Taiwan-1008DHF AY776328 2 Ven2AF100465 3 D3-H-IMTSSA-MART-1999-1243 AY099337 3D3-H-IMTSSA-SRI-2000-1266 AY099336 3 80-2 AF317645 3 98901403 AB189125 398901437 AB189126 3 98901517 AB189127 3 98902890 AB189128 3 BA51AY858037 3 BDH02-1 AY496871 3 BDH02-3 AY496873 3 BDH02-4 AY496874 3BDH02-7 AY496877 3 BR74886-02 AY679147 3 C0331-94 AY876494 3 C0360-94AY923865 3 den3_88 AY858038 3 den3_98 AY858039 3 FW01 AY858040 3 FW06AY858041 3 H87 NC_001475 3 D3-HU-TL018NIID-2005 AB214879 3D3-HU-TL029NIID-2005 AB214880 3 D3-HU-TL109NIID-2005 AB214881 3D3-HU-TL129NIID-2005 AB214882 3 InJ_16_82 DQ401690 3 KJ30i AY858042 3KJ46 AY858043 3 KJ71 AY858044 3 mutant BDH02_01 DQ401689 3 mutantBDH02_03 DQ401691 3 mutant BDH02_04 DQ401692 3 mutant BDH02_07 DQ4016933 mutant tnJ_16_82 DQ401694 3 mutant PhMH_J1_97 DQ401695 3 PF89-27643AY744677 3 PF89-320219 AY744678 3 PF90-3050 AY744679 3 PF90-3056AY744680 3 PF90-6056 AY744681 3 PF92-2956 AY744682 3 PF92-2986 AY7446833 PH86 AY858045 3 PhMH-J1-97 AY496879 3 PI64 AY858046 3 SingaporeAY662691 3 Singapore 8120-95 AY766104 3 Sleman-78 AY648961 3 TB16AY858047 3 TB55i AY858048 3 ThD3_0007_87 AY676353 3 ThD3_0010_87AY676353 3 ThD3_0055_93 AY676351 3 ThD3_0104_93 AY676350 3 ThD3_1283_98AY676349 3 ThD3_1687_98 AY676348 3 PF92-4190 AY744684 3 PF94-136116AY744685 3 Taiwan-739079A AY776329 4 2A AF375822 4 Recombinant clonerDEN4 AF326825 4 2Adel30 AF326826 4 814669 AF326573 4 B5 AF289029 4rDEN4del30 AF326827 4 H241 AY947539 4 rDEN4 NC_002640 4 Singapore8976-95 AY762085 4 SW38i AY858050 4 ThD4_0017_97 AY618989 4 ThD4_0087_77AY618991 4 ThD4_0348_91 AY618990 4 ThD4_0476_97 AY618988 4 ThD4_0485_01AY618992 4 ThD4_0734_00 AY618993 4 Taiwan-2K0713 AY776330 4 UnknownM14931

Mutations can be made in the 3′-UTR of a wild type infectious clone,e.g., dengue virus serotype 3, strain Sleman/78 or an infectious cloneof another wild type, virulent dengue virus, and the mutants can then betested in an animal model system (e.g., in mouse and/or monkey modelsystems) to identify sites that cause attenuation. Attenuation is judgedby, for example, detection of decreased viremia. One or more additionalmutations found to attenuate the wild-type virus are optionallyintroduced into a wild type dengue virus, and these mutants are testedin an animal model system (e.g., in a mouse and/or a monkey modelsystem) to determine whether the resulting mutants are attenuated.Mutants that are found to be attenuated can then be used as new vaccinestrains that have increased safety, due to attenuation.

In addition to the viruses listed above, dengue viruses includingchimeric dengue viruses that include one or more attenuating mutationsare included in the invention. These chimeras can consist of a denguevirus of a first serotype (i.e., a background dengue virus) in which astructural protein (or proteins) has been replaced with a correspondingstructural protein (or proteins) of a dengue virus of a second serotype.For example, the chimeras can consist of a background dengue virus inwhich the prM and E proteins of the dengue virus of the first serotypehave been replaced with the prM and E proteins of the dengue virus ofthe second serotype. The chimeric viruses can be made from anycombination of dengue viruses of different serotypes. The dengue virusagainst which immunity is sought is the source of the insertedstructural protein(s).

As is noted above, mutations that are included in the viruses of thepresent invention are attenuating. These mutations are present in thedengue virus 3′-UTR structure to attenuate the virus. Mutations can bemade in the 3′-UTR using standard methods, such as site-directedmutagenesis. One example of the type of mutation present in the virusesof the invention is substitutions, but other types of mutations, such asdeletions and insertions, can be used as well. In addition, as is notedabove, the mutations can be present singly or in the context of one ormore additional mutations.

Referring to FIG. 1, two approaches were taken to attenuate denguevirus. In one aspect, nucleotides additional to the Δ30 mutation weredeleted from the 3′-UTR. In another aspect, the 3-UTR of a dengue virusof a first serotype was replaced with the 3′-UTR from a dengue virus ofa second serotype (optionally containing the Δ30 mutation andnucleotides additional to the Δ30 mutation deleted from the 3′-UTR).

Deletion of Nucleotides Additional to the Δ30 Mutation from the 3′-UTR

Referring to FIGS. 2-5, using the first approach, the 3′-UTR of dengueviruses contain various conserved sequence motifs. The sequence of theDEN4 3′-UTR is illustrated in FIG. 5. The genome of DEN4 strain 814669contains 10,646 nucleotides, of which the last 384 nt at the 3′ terminusare untranslated (non-coding). The locations of various sequencecomponents in this region are designated with the reverse-directionnumbering system. These sequences include the 3′ distal secondarystructure (nt 1 to 93), predicted to form stem-loop 1 (SL-1), whichcontains terminal loop 1 (TL-1). Nucleotides 117-183 form stem-loop 2(SL-2) which contains TL-2. Nucleotides 201-277 form a pair ofstem-loops (SL-3) which in part contains TL-3. Although the primarysequence of stem-loop 1 differs slightly among the dengue serotypes, thesecondary structure is strictly conserved (compare FIGS. 2-5). Althoughthe nucleotide spacing between SL-2 and neighboring SL-1 and SL-3 differamong the dengue virus serotypes, the overall structure of SL-2 iswell-conserved. In addition, the exposed 9 nucleotides that compriseTL-2 are identical within all 4 dengue serotypes. It is TL-2 and itssupporting stem structure that are removed by the Δ30 mutation (about nt143-172). Removal of these 30 nucleotides results in formation of a newpredicted structural element (SL-2Δ30) which has a primary sequence andsecondary structure which is identical for each of the dengue virusserotypes (compare FIGS. 6-9).

FIGS. 10-13 illustrate the approach where nucleotides additional to theΔ30 mutation are deleted from the 3′-UTR. The Δ30 mutation removes theTL-2 homologous structure in each of the dengue virus serotypes 1, 2, 3,and 4. The approach where nucleotides additional to the Δ30 mutation aredeleted from the 3′-UTR removes the TL-2 homologous structure andsequence up to and optionally including the TL-3 homologous structure sothat the deletion extends as far as the 5′ boundary of the TL-3homologous structure in each of the dengue virus serotypes 1, 2, 3, and4. In the approach illustrated in FIGS. 10-14, an additional deletion ofabout 31 nucleotides from TL-3 results in formation of a new predictedstructural element (SL-3Δ31).

Referring to FIGS. 14-17, the Δ86 mutation removes the TL-2 homologousstructure and removes sequence up to the TL-3 homologous structure ineach of the dengue virus serotypes DEN1, DEN2, DEN3 and DEN4. Thisdeletion results in the formation of a new predicted structural element(SL-2Δ86).

In some embodiments that involve deletion of nucleotides additional tothe Δ30 mutation, nucleic acid deletions are made to the 3′-UTRstructure of the dengue virus genome to attenuate the virus whilemaintaining its immunogenicity. The deletions include the Δ30 deletion(nt 173-143 of the serotype 3 Sleman/78 strain in an exemplary manner orcorresponding thereto in other strains of DEN1, DEN2, DEN3, or DEN4;numbering is from the 3′ end of the viral genome) in addition todeletion of additional 3′-UTR sequence that is contiguous ornon-contiguous to the Δ30 deletion. The Δ30 deletion corresponds to theTL-2 structure of the 3′-UTR. One type of embodiment, termedrDEN1Δ30/31, rDEN2Δ30/31, rDEN3Δ30/31, or rDEN4Δ30/31 includes theoriginal Δ30 deletion and a non-contiguous 31 nt deletion that removesboth the original TL-2 and TL-3 structures. Another type of embodiment,termed rDEN1Δ61, rDEN2Δ61, rDEN3Δ61, or rDEN4Δ61 includes the Δ30deletion and deletion of 31 contiguous nucleotides extending 3′ from theΔ30 deletion. Another type of embodiment, termed rDEN1Δ86, rDEN2Δ86,rDEN3Δ86, or rDEN4Δ86, includes the Δ30 deletion and deletion of 56contiguous nucleotides extending 5′ from the Δ30 deletion. For DEN3, acomplete list of mutant viruses constructed to contain 3′-UTR deletionmutations is presented below in Table 2.

Replacement of the 3′-UTR of a Dengue Virus of a First Serotype with the3′-UTR from a Dengue Virus of a Second Serotype

Using the second approach, the 3′-UTR of rDEN3 may be replaced with the3′-UTR of rDEN4, optionally containing the Δ30 mutation and nucleotidesadditional to the Δ30 mutation deleted from the 3′-UTR. Other examplesinclude replacement of the 3′-UTR of rDEN3 with the 3′-UTR of denguevirus serotypes 1 and 2, optionally containing the Δ30 mutation andnucleotides additional to Δ30 mutation deleted from the 3′-UTR. Otherexamples include: replacement of the 3′-UTR of rDEN1 with the 3′-UTR ofdengue virus serotypes 2, 3, and 4, optionally containing the Δ30mutation and nucleotides additional to the Δ30 mutation deleted from the3′-UTR; replacement of the 3′-UTR of rDEN2 with the 3′-UTR of denguevirus serotypes 1, 3, and 4, optionally containing the Δ30 mutation andnucleotides additional to the Δ30 mutation deleted from the 3′-UTR; and,replacement of the 3′-UTR of rDEN4 with the 3′-UTR of dengue virusserotypes 1, 2, and 3, optionally containing the Δ30 mutation andnucleotides additional to the Δ30 mutation deleted from the 3′-UTR.

Embodiments that involve replacement of the 3′-UTR of a dengue virus ofa first serotype with the 3′-UTR of dengue virus of a second serotypeinclude:

a) rDEN1-3′D2, rDEN1-3′D2x, rDEN1-3′D3, rDEN1-3′D3x, rDEN1-3′D4,rDEN1-3′D4x:

rDEN1/2-3′D1, rDEN1/2-3′D1x, rDEN1/2-3′D3, rDEN1/2-3′D3x, rDEN1/2-3′D4,rDEN1/2-3′D4x;rDEN1/3-3′D1, rDEN1/3-3′ rDEN1/3-3′D2, rDEN1/3-3′D2x, rDEN1/3-3′D4,rDEN1/3-3′D4x;rDEN1/4-3 D1, rDEN1/4-3′D1x, rDEN1/4-3′D2, rDEN1/4-3′D2x, rDEN1/4-3′D3,rDEN1/4-3′D3x;

b) rDEN2-3′D1, rDEN2-3′D1x, rDEN2-3′D3, rDEN2-3′D3x, rDEN2-3′D4,rDEN2-3′ D4x;

rDEN2/1-3′D2, rDEN2/1-3′D2x, rDEN2/1-3′D3, rDEN2/1-3′D3x, rDEN2/1-3′D4,rDEN2/1-3′D4x; rDEN2/3-3′D1, rDEN2/3-3′D1x, rDEN2/3-3′D2, rDEN2/3-3′D2x,rDEN2/3-3′D4, rDEN2/3-3′D4x; rDEN2/4-3′D1, rDEN2/4-3′D1x, rDEN2/4-3′D2,rDEN2/4-3′D2x, rDEN2/4-3′D3, rDEN2/4-3′D3x;

c) rDEN3-3′D1, rDEN3-3″D1x, rDEN3-3′D2, rDEN3-3′D2x, rDEN3-3′D4,rDEN3-3′D4x;

rDEN3/1-3′D2, rDEN3/1-3′D2x, rDEN3/1-3′D3, rDEN3/1-3′D3x, rDEN3/1-3 D4,rDEN3/1-3′ D4x;rDEN3/2-3′D1, rDEN3/2-3′D1x. rDEN3/2-3′D3, rDEN3/2-3′D3x, rDEN3/2-3″D4,rDEN3/2-3′D4x;rDEN3/4-3′D1, rDEN3/4-3x, rDEN3/4-3′D2, rDEN3/4-3′D2x, rDEN3/4-3′D3,rDEN3/4-3′D3x; and

d) rDEN4-3′D1, rDEN4-3′D1x, rDEN4-3′D2, rDEN4-3′D2x, rDEN4-3′D3,rDEN4-3′D3x;

rDEN4/1-3′D2, rDEN4/1-3′D2x, rDEN4/1-3′D3, rDEN4/1-3′D3x, rDEN4/1-3′D4,rDEN4/1-3D4x;rDEN4/2-3′D1, rDEN4/2-3 D1x, rDEN4/2-3′D3, rDEN4/2-3′D3x, rDEN4/2-3′D4,rDEN4/2-3′D4x;rDEN4/3-3′D1, rDEN4/3-3″ D1x, rDEN4/3-3′D2, rDEN4/3-3 D2 x, rDEN4/3-3″D4, rDEN4/3-3′D4x;where x is a mutation listed in Table 2.

Method of Making and Using Dengue or Chimeric Dengue Viruses

The viruses (including chimeric viruses) of the present invention can bemade using standard methods in the art. For example, an RNA moleculecorresponding to the genome of a virus can be introduced into hostcells, e.g., Vero cells, from which (or the supernatants of which)progeny virus can then be purified. In this method, a nucleic acidmolecule (e.g., an RNA molecule) corresponding to the genome of a virusis introduced into the host cells, virus is harvested from the medium inwhich the cells have been cultured, and the virus is formulated for thepurposes of vaccination.

The viruses of the invention can be administered as primary prophylacticagents in adults or children at risk of infection, or can be used assecondary agents for treating infected patients. For example, in thecase of DEN virus and chimeric DEN viruses, the vaccines can be used inadults or children at risk of DEN virus infection, or can be used assecondary agents for treating DEN virus-infected patients. Examples ofpatients who can be treated using the DEN virus-related vaccines andmethods of the invention include (i) children in areas in which DENvirus is endemic, (ii) foreign travelers, (iii) military personnel, and(iv) patients in areas of a DEN virus epidemic. Moreover, inhabitants ofregions into which the disease has been observed to be expanding (e.g.,beyond Sri Lanka, East Africa and Latin America), or regions in which itmay be observed to expand in the future can be treated according to theinvention.

Formulation of the viruses of the invention can be carried out usingmethods that are standard in the art. Numerous pharmaceuticallyacceptable solutions for use in vaccine preparation are well known andcan readily be adapted for use in the present invention by those ofskill in this art (see, e.g., Remington's Pharmaceutical Sciences (18thedition), ed. A. Gennaro, 1990, Mack Publishing Co., Easton, Pa.). Theviruses can be diluted in a physiologically acceptable solution, such assterile saline, sterile buffered saline, or L-15 medium. In anotherexample, the viruses can be administered and formulated, for example, asa fluid harvested from cell cultures infected with dengue virus orchimeric dengue virus.

The vaccines of the invention can be administered using methods that arewell known in the art, and appropriate amounts of the vaccinesadministered can readily be determined by those of skill in the art. Forexample, the viruses of the invention can be formulated as sterileaqueous solutions containing between 10² and 10⁷ infectious units (e.g.,plaque-forming units or tissue culture infectious doses) in a dosevolume of 0.1 to 1.0 ml, to be administered by, for example,intramuscular, subcutaneous, or intradermal routes. Further, thevaccines of the invention can be administered in a single dose or,optionally, administration can involve the use of a priming dosefollowed by a booster dose that is administered, e.g., 2-6 months later,as determined to be appropriate by those of skill in the art.

Optionally, adjuvants that are known to those skilled in the art can beused in the administration of the viruses of the invention. Adjuvantsthat can be used to enhance the immunogenicity of the viruses include,for example, liposomal formulations, synthetic adjuvants, such as (e.g.,QS21), muramyl dipeptide, monophosphoryl lipid A, or polyphosphazine.Although these adjuvants are typically used to enhance immune responsesto inactivated vaccines, they can also be used with live vaccines.

Nucleic Acid Sequences

Nucleic acid sequences of DEN viruses are useful for designing nucleicacid probes and primers for the detection of deletion or chimeric3′-UTRs in a sample or specimen with high sensitivity and specificity.Probes or primers corresponding to deletion or chimeric 3′-UTRs can beused to detect the presence of deletion or chimeric 3′-UTRs in generalin the sample, to quantify the amount of deletion or chimeric 3′-UTRs inthe sample, or to monitor the progress of therapies used to treat DENvirus infection. The nucleic acid and corresponding amino acid sequencesare useful as laboratory tools to study the organisms and diseases andto develop therapies and treatments for the diseases.

Nucleic acid probes and primers selectively hybridize with nucleic acidmolecules encoding deletion or chimeric 3″-UTRs or complementarysequences thereof. By “selective” or “selectively” is meant a sequencewhich does not hybridize with other nucleic acids to prevent adequatedetection of the deletion or chimeric 3-UTRs. Therefore, in the designof hybridizing nucleic acids, selectivity will depend upon the othercomponents present in the sample. The hybridizing nucleic acid shouldhave at least 70% complementarity with the segment of the nucleic acidto which it hybridizes. As used herein to describe nucleic acids, theterm “selectively hybridizes” excludes the occasional randomlyhybridizing nucleic acids, and thus has the same meaning as“specifically hybridizing.” The selectively hybridizing nucleic acidprobes and primers of this invention can have at least 70%, 80%, 85%,90%, 95%, 97%, 98% and 99% complementarity with the segment of thesequence to which it hybridizes, preferably 85% or more.

The present invention also contemplates sequences, probes and primersthat selectively hybridize to the encoding nucleic acid or thecomplementary, or opposite, strand of the nucleic acid. Specifichybridization with nucleic acid can occur with minor modifications orsubstitutions in the nucleic acid, so long as functional species-specieshybridization capability is maintained. By “probe” or “primer” is meantnucleic acid sequences that can be used as probes or primers forselective hybridization with complementary nucleic acid sequences fortheir detection or amplification, which probes or primers can vary inlength from about 5 to 100 nucleotides, or preferably from about 10 to50 nucleotides, or most preferably about 18-24 nucleotides. Isolatednucleic acids are provided herein that selectively hybridize with thespecies-specific nucleic acids under stringent conditions and shouldhave at least five nucleotides complementary to the sequence of interestas described in Molecular Cloning: A Laboratory Manual, 2^(nd) ed.,Sambrook, Fritsch and Maniatis, Cold Spring Harbor Laboratory, ColdSpring Harbor, N.Y., 1989.

If used as primers, the composition preferably includes at least twonucleic acid molecules which hybridize to different regions of thetarget molecule so as to amplify a desired region. Depending on thelength of the probe or primer, the target region can range between 70%complementary bases and full complementarity and still hybridize understringent conditions. For example, for the purpose of detecting thepresence of deletion or chimeric 3′-UTRs, the degree of complementarilybetween the hybridizing nucleic acid (probe or primer) and the sequenceto which it hybridizes is at least enough to distinguish hybridizationwith a nucleic acid from other organisms.

The nucleic acid sequences of the invention include a diagnostic probethat serves to report the detection of a cDNA amplicon amplified fromthe viral genomic RNA template by using areverse-transcription/polymerase chain reaction (RT-PCR), as well asforward and reverse amplimers that are designed to amplify the cDNAamplicon. In certain instances, one of the amplimers is designed tocontain a vaccine virus-specific mutation at the 3′-terminal end of theamplimer, which effectively makes the test even more specific for thevaccine strain because extension of the primer at the target site, andconsequently amplification, will occur only if the viral RNA templatecontains that specific mutation.

Automated PCR-based nucleic acid sequence detection systems have beenrecently developed. TaqMan assay (Applied Biosystems) is widely used. Amore recently developed strategy for diagnostic genetic testing makesuse of molecular beacons (Tyagi and Kramer 1996 Nature Biotechnology14:303-308). Molecular beacon assays employ quencher and reporter dyesthat differ from those used in the TaqMan assay. These and otherdetection systems may be used by one skilled in the art.

Dengue Virus Type 3 (DEN3) Vaccine Components Generated by Introductionof Deletions in the 3′ Untranslated Region (UTR) or Exchange of the DEN33′-UTR with that of DEN4

There are four dengue virus serotypes (DEN1, DEN2, DEN3, and DEN4) whichcirculate in tropical and subtropical regions of the world inhabited bymore than 2.5 billion people (Gubler D J 1998 Clin Microbiol Rev11:480-496). DEN viruses are endemic in at least 100 countries and causemore human disease than any other arbovirus. Annually, there are anestimated 50-100 million dengue infections and hundreds of thousands ofcases of dengue hemorrhagic fever/shock syndrome (DHF/DSS), withchildren bearing much of the disease burden (Gubler D J and Meltzer M1999 Adv Virus Res 53:35-70). DHF/DSS remains a leading cause ofhospitalization and death of children in at least eight southeast Asiancountries (World Health Organization 1997 Dengue Haemorrhagic Fever:Diagnosis, Treatment, Prevention and Control, 2^(nd) edition, WHO,Geneva). The dramatic increase in both the incidence and severity ofdisease caused by the four DEN serotypes over the past two decades isdue in large part to the geographic expansion of the mosquito vectors,Aedes aegypti and Aedes albopictus, and the increased prevalence of thefour DEN serotypes (Gubler D J 1998 Clin Microbiol Rev 11:480-496). Thedengue viruses are maintained in a life cycle of transmission frommosquito to human to mosquito with no other apparent viral reservoirparticipating in this life cycle in urban settings (Rice C M, 1996 inFlaviviridae: The viruses and their replication, Fields B N, Knipe D M,Howley P M, Chanock R M, Melnick J L, Monath T P, Roizman B, Straus S E,eds. Fields Virology. Philadelphia: Lippincott-Raven Publishers, pp.931-959).

The DEN viruses, members of the Flaviviridae family, have sphericalvirions of approximately 40 to 60 nm which contain a single-strandedpositive-sense RNA genome. A single polypeptide is co-translationallyprocessed by viral and cellular proteases generating three structuralproteins (capsid C, membrane M, and envelope E) and at least sevennon-structural (NS) proteins. The genome organization of the DEN virusesis 5% UTR-C-prM-E-NS1-NS2A-NS2B-NS3-NS4A-NS4B-NS5-UTR-3′(UTR-untranslated region, prM-membrane precursor) (Rice C M, 1996 inFlaviviridae: The viruses and their replication, Fields B N, Knipe D M,Howley P M, Chanock R M, Melnick J L, Monath T P, Roizman B, Straus S E,eds. Fields Virology. Philadelphia: Lippincott-Raven Publishers, pp.931-959).

In response to the increasing incidence and severity of DEN infection,development of vaccines is being pursued to prevent DEN virus disease.An economical vaccine that prevents disease caused by the DEN viruseshas become a global public health priority. The cost-effectiveness,safety, and long-term efficacy associated with the live attenuatedvaccine against yellow fever (YF) virus, another mosquito-borneflavivirus, serves as a model for the feasibility of developing of alive attenuated DEN virus vaccine (Monath T P, 1999 in Yellow fever,Plotkin S A, Orenstein W A, eds. Vaccines, Philadelphia: W.B. SaundersCo., 815-879). Additionally, an effective live attenuated Japaneseencephalitis (JE) virus vaccine is used in Asia, and inactivated virusvaccines are available for JE and tick-borne encephalitis virus. Theneed for a vaccine against the DEN viruses is mounting, and, despitemuch effort, the goal of developing a safe and efficacious DEN virusvaccine has yet to be attained. An effective DEN virus vaccine mustconfer protection from each serotype because all four serotypes commonlycirculate in endemic regions and secondary infection with a heterologousserotype is associated with increased disease severity.

We have employed two strategies for generating live attenuated vaccinecomponents against each serotype that can then be combined intotetravalent formulations (Blaney J E et al. 2006 Viral Immunol.19:10-32). First, reverse genetics has been used to introduce anattenuating 30 nucleotide deletion (Δ30) mutation into the 3′-UTR ofcDNA clones of each DEN serotype (Durbin, A P et al. 2001 Am J Trop MedHyg 65:405-413; Whitehead S S et al. 2003 J Virol 77:1653-1657; Blaney JE et al. 2004 Am J Trop Med Hyg 71:811-821; Blaney J E et al 2004 BMCInf Dis 4:39). Initially, the rDEN4Δ30 vaccine component was found to beattenuated in rhesus monkeys (Table 1) and phase I/II clinical trials inhumans have demonstrated that virus infection results in low viremia, isstrongly immunogenic, and exhibits minimal reactogenicity with noobservation of serious adverse events (Durbin, A. P. et al. 2001 Am JTrop Med Hyg 65:405-413; Durbin et al. 2005 J Inf Dis 191:710-718).Recently, the rDEN1Δ30 vaccine component, which was also attenuated inrhesus monkeys (Table 1), has been found to share a similar phenotype inclinical trials as that observed for rDEN4Δ30; low viremia, strongimmunogenicity, and minimal reactogenicity in 20 volunteers (Whitehead SS et al. 2003 J Virol 77:1653-1657; Blaney J E et al. 2006 ViralImmunol. 19:10-32). Unfortunately, the rDEN2Δ30 and rDEN3Δ30 vaccinecomponents did not appear to be satisfactorily attenuated in rhesusmonkeys during pre-clinical testing and there is no plan to test thesein humans (Table 1) (Blaney J E et al. 2004 Am J Trop Med Hyg71:811-821; Blaney J E et al. 2004 BMC Inf Dis 4:39). Consequently, analternative strategy for vaccine development has been generation ofantigenic chimeric viruses by replacement of structural proteins of theattenuated rDEN4Δ30 vaccine component with those from DEN2 or DENSyielding the rDEN2/4430 and rDEN3/4Δ30 vaccine components, respectively(Whitehead S S et al. 2003 Vaccine 21:4307-4316; Blaney J E et al. 2004Am J Trop Med Hyg 71:811-821). The rDEN2/4430 vaccine virus has beentested in humans and appears safe and strongly immunogenic, whileclinical evaluation of the rDEN3/4Δ30 virus is currently planned.

TABLE 1 Effects of the Δ30 mutation on the four DEN serotypes in rhesusmonkeys Viremia^(a) Mean no. of Geometric % of viremic Mean peak meanviremic days per virus titer neutralizing Virus monkeys monkey(log₁₀PFU/ml ± SE) antibody titer^(b) Reference rDEN1 100 2.8 2.1 ± 0.11,230 Whitehead et al. rDEN1Δ30 50 0.5 0.8 ± 0.1 780 J. Virol, 2003,77:1653 rDEN2 100 4.0 1.9 ± 0.1 173 Blaney et al. BMC Inf rDEN2Δ30 1002.8 1.7 ± 0.2 91 Dis., 2004, 4:39 rDEN3 100 2.3 1.4 ± 0.2 363 Blaney etal. Am. J. rDEN3Δ30 100 2.0 1.5 ± 0.2 265 Trop. Med. Hyg., 2004, 71:811rDEN4 100 3.0 2.2 ± 0.2 322 Hanley et al. rDEN4Δ30 100 2.0 1.4 ± 0.2 154Vaccine, 2004, 22:3440 ^(a)Groups of rhesus monkeys were inoculatedsubcutaneously with 5.0 log₁₀ PFU of the indicated virus in a 1 ml dose.Serum was collected daily for 10 days. Virus titer in serum wasdetermined by plaque assay in Vero cells. ^(b)Plaque reduction (60%)neutralizing antibody titers were determined on day 28 serum usingindicated wild type virus. Reciprocal dilution of geometric mean isindicated.

Here, we describe novel vaccine components for the DEN3 serotypegenerated by genetic modification of the 3′-UTR of the DEN3 cDNA clone(Blaney J E et al. 2004 Am J Trop Med Hyg 71:811-821). Development ofthese DEN3 vaccine components, which possess the full complement of wildtype DEN3 proteins, is important for two reasons. First, the presentvaccine component for DEN3, rDEN3/4Δ30, may be found to be under- orover-attenuated in clinical trials. Second, an optimal vaccine forconferring protection from disease caused by DEN3 may require inductionof T cell responses against the entire set of DEN3 proteins, rather thanjust the M and E which are the only DEN3 sequences present in therDEN3/4Δ30 chimeric virus. To generate additional DEN3 vaccinecomponents, novel deletions which encompass or border the Δ30 deletionin the 3′-UTR were introduced into the rDEN3 cDNA clone. Alternatively,the 3′-UTR of the rDEN3 cDNA clone was replaced with that of rDEN4 orrDEN4Δ30. Viable viruses were analyzed for attenuation phenotypes intissue culture, SCID mice transplanted with HuH-7 cells, and rhesusmonkeys. Three mutant viruses (rDEN3Δ30/31, rDEN3Δ86, and rDEN3-3′D4Δ30)have preclinical phenotypes which suggest they may be safe andimmunogenic in humans.

Generation of rDEN3 Deletion Mutants

We sought to generate expanded deletion mutations which include theoriginal Δ30 (nt 173-143) mutation. Table 2 lists seven deletionmutations which encompass the original Δ30 mutation including Δ50, Δ61,Δ80, Δ86, Δ116A, Δ116B, and Δ146. In addition, the Δ30/31 mutationincludes the original Δ30 mutation and a non-contiguous 31 nt deletion.The Δ31 mutation was also generated alone to discern the contribution ofeither Δ30 or Δ31 in the combined Δ30/31 deletion mutation. The locationof bordering nucleotides of deletions in the predicted secondarystructure of the DEN3 3′-UTR are indicated in FIG. 4. In addition, thepredicted secondary structure of the DEN3 3′-UTR for rDEN3Δ30,rDEN3Δ30/31, and rDEN3Δ86 are indicated in FIGS. 8, 12, and 16,respectively.

TABLE 2 Deletion mutations created in the 3′-UTR of DEN3 Slernan/78Deleted Deletion Mutation nucleotides^(a) junction Δ30 173-143-CCAAΔGACU- Δ31 258-228 -CUGCΔGACU- Δ50 192-143 -CACAΔGACU- Δ61 173-113-CCGAΔUAAA- Δ80 192-113 -CACAΔUAAA- Δ86 228-143 -UAGCΔGACU- Δ116 (A)228-113 -UAGCΔUAAA- Δ116 (B) 258-143 -CUCCΔGACU- Δ146 258-113-CUGCΔUAAA- Δ30/31 173-143 -CCAAΔGACU- 258-228 -CUGCΔGACU- ^(a)Numberingis from the 3′-end of viral genome

PCR mutagenesis was used to introduce the nine new deletion mutationsinto the DEN3 Sleman/78 cDNA plasmid, p3, which was previously used togenerate the rDEN3Δ30 vaccine component (Blaney J E et al. 2004 Am JTrop Med Hyg 71:811-821). The p3-frag.4 cDNA subclone was used as thetemplate for PCR reactions with indicated pairs of mutagenicoligonucleotides listed in Table 3, except for the Δ30/31 deletionmutation which used p3-frag.4Δ30 cDNA subclone as a template. PCRproducts were ligated and used to transform competent bacterial cells.Plasmid DNA was isolated from bacterial clones and the presence of theappropriate deletion mutation was confirmed by sequence analysis. Togenerate intact DEN3 cDNA plasmids containing the deletion mutations,the KpnI-PstI fragment (963 nt) from the mutated p3-frag.4 cDNAsubclones were introduced into the p3-7164 cDNA plasmid. The p3-7164plasmid encodes the 7164 Vero cell adaptation mutation which hadpreviously been shown to enhance growth and transfection efficiency inVero cells (Blaney J E et al. 2004 Am J Trop Med Hyg 71:811-821). Fulllength p3 plasmids containing the deletion mutations were confirmed tocontain the correct 3′-UTR sequence. Mutations in addition to theengineered deletions were identified in the rDEN3Δ30/31 and rDEN3486viruses when compared to the DEN3 p3 plasmid cDNA (Genbank #AY656169)(Table 4).

TABLE 3 Mutagenic primer sequences for construction of 3′-UTR deletionsPrimer name Sequence (5′→3′) 113F TAAAAACAGCATATTGACGCTGGGAG(SEQ ID NO: 24) 143F GACTAGAGGTTAGAGGAGAC (SEQ ID NO: 25) 228FGACTAGCGGTTAGAGGAGACCCC (SEQ ID NO: 26) 1738TCGGGCCCCGCTGCTGCGTTG (SEQ ID NO: 27) 173RTTGGGCCCCGCTGCTGCGTTG (SEQ ID NO: 28) (for Δ30) 192RTGTGTCATGGGAGGGGTCTC (SEQ ID NO: 29) 228RGCTACACCGTGCGTACAGCTTCC (SEQ ID NO: 30) 258RGCAGCCTCCCAGGTTTTACGTCC (SEQ 1D NO: 31)

TABLE 4 Mutations in addition to the engineered deletions thatwere identified in the rDEN3Δ30/31 and rDEN3Δ86 viruses whencompared to the DEN3 p3 plasmid cDNA (Genbank #AY656169) NucleotideNucleotide Amino acid Amino acid Virus Gene position substitutionposition change rDEN3Δ30/31 NS4B  7164^(a) U → C 115 Val → Ala NS4B 7398 C → U 193 Ala → Val rDEN3Δ86 M   512 A → G  26 Lys → Glu NS3  6076C → U 521 silent NS4B  7164^(a) U → C 115 Val → Ala NS5  8623 U → C 353silent NS5 10267^(b) A → U END end → Tyr 3′-UTR 10455 G → C — — ^(a)The7164 mutation is a Vero cell adaptation mutation which was engineeredinto the cDNA construct. ^(b)There is a mixed population at this ntposition (A→A/U) that changes the stop codon (UAA) at the end of NS5 toUAU which encodes Tyr. This would serve to extend NS5 by 2 amino acids(Tyr-Thr-End) because a stop codon remains at nts 10271-10273.

For recovery of viruses, 5′-capped RNA transcripts were synthesized invitro from cDNA plasmids and transfected into either Vero cells or C6/36cells. Prior to transcription and generation of infectious virus, thelinker sequences were removed from cDNA plasmids by digestion with SpeI.Plasmids were then recircularized by ligation, linearized with Acc651(isoschizomer of KpnI which cleaves leaving only a single 3′nucleotide), and transcribed in vitro using SP6 polymerase. Purifiedtranscripts were then transfected into Vero or C6/36 cells.

Recombinant viruses encoding each of the nine mutations, Δ30/31, Δ31,Δ50, Δ61, Δ80, Δ86, Δ116A, Δ116B, and Δ146, were successfully recoveredin C6/36 cells, while only rDENΔ31 was recovered in Vero cells. TherDEN3 deletion mutant viruses were then passaged once in Vero cellsfollowed by biological cloning by two terminal dilutions in Vero cells.Cloned viruses were then passaged two to seven times in Vero cells in anattempt to reach a stock titer of at least 6.0 log₁₀PFU/ml which isconsidered sufficient to allow for cost-effective manufacture. Threerecombinant viruses (rDEN3Δ50, rDEN3Δ116A, and rDEN3Δ146) were found tobe excessively restricted for replication in Vero cells, despite beingviable. Therefore, these three viruses were not studied further. Thegenetic sequence of the 3′-UTR was determined for the six remainingdeletion mutant viruses that reached peak virus titers of at least 6.0log₁₀PFU/ml. The correct 3′-UTR sequence with the appropriate deletionwas found for rDEN3Δ61, rDEN3Δ80, rDEN3Δ86 and rDEN3Δ30/31. However, twomutant viruses were found to contain additional deletions or mutationsand were deemed to potentially have unstable genotypes. First, rDEN3Δ31had the correct 3′-UTR deletion of nt 258-228 but also contained a 25 ntdeletion of nt 222-198. Second, rDEN3Δ116B had the correct 3′-UTRdeletion of nt 258-143 but also contained a 8 nt deletion of nt 430-423and a single A->G substitution at nt 265. The potential of geneticinstability with these viruses precludes their use as vaccine componentsso they were not further studied. Therefore, of the nine originaldeletions constructed, four mutant viruses were found to replicateefficiently in Vero cells and were studied further; rDEN3Δ61, rDEN3Δ80,rDEN3Δ86 and rDEN3Δ30/31.

Generation of rDEN3 Chimeric Viruses with the 3′-UTR Derived from rDEN4or rDEN4Δ30

Another strategy was employed to generate novel rDEN3 vaccinecomponents; replacement of the 3′-UTR of the rDEN3 cDNA clone with thatof rDEN4 or rDEN4Δ30 (FIG. 18A). The 3′-UTR chimeric virus,rDEN3-3′D4Δ30, was designed to be a vaccine component for inclusion intetravalent formulations which share the Δ30 deletion mutation among allfour serotypes. The rDEN3-3 D4 virus was designed to discern thecontribution of the 3′-UTR chimerization and the Δ30 mutation to anyobserved phenotypes.

The p3-3′D4Δ30 plasmid was generated as follows. First, PCR mutagenesiswas used to introduce a HpaI restriction site into the p3-frag.4 cDNAsubclone (FIG. 18B). PCR products were ligated and used to transformcompetent bacterial cells. Plasmid DNA was isolated from bacterialclones and the presence of the appropriate deletion mutation wasconfirmed by sequence analysis. To introduce the rDEN4Δ30 3′-UTR intothe p3-frag.4(HpaI) cDNA subclone, a 364 nt fragment encompassing thep4Δ30 3′-UTR was amplified by PCR using a forward primer(5′AACAACAACAAACACCAAAGGCTATTG-3′, SEQ ID NO: 32) and reverse primer(5′-CCTACCGGTACCAGAACCTGTTG-3′, SEQ ID NO: 33). To generate thep3-frag.4-3′D4Δ30 cDNA subclone, the HpaI-KpnI fragment was removed fromp3-frag.4(HpaI) and replaced with the p4Δ30 3′-UTR PCR fragment whichhad been cleaved by KpnI. The PstI-KpnI fragment of p3-frag.4-3′D4Δ30was introduced into the p3 plasmid to make the full length cDNA clone,p3-3′D4Δ30. The sequence of the 3′-UTR and NS5 junction were confirmedto be correct.

To generate p3-3′D4, the 30 deleted nucleotides of the Δ30 deletionmutation were introduced into the p3-frag.4-3′D4Δ30 subclone. Briefly,the MluI-KpnI fragment of p3-frag.4-3′D4Δ30, which encompasses the Δ30region, was replaced with the corresponding fragment of p4 to make theplasmid, p3-frag.4-3′D4. To generate a full length p3 genome, thePstI-KpnI fragment of p3 was replaced with the corresponding fragment ofp3-frag.4-3′D4. The 3′-UTR sequence of the p3-3′D4 plasmid wasdetermined to be correct and contained the missing 30 nt of the Δ30mutation.

For recovery of viruses, 5′-capped RNA transcripts were synthesized invitro from cDNA plasmids and transfected into either Vero cells or C6/36cells. Prior to transcription and generation of infectious virus, thelinker sequences were removed from cDNA plasmids by digestion with SpeI.Plasmids were then recircularized by ligation, linearized with Acc651(isoschizomer of KpnI which cleaves leaving only a single 3′nucleotide), and transcribed in vitro using SP6 polymerase. Purifiedtranscripts were then transfected into Vero or C6/36 cells.

rDEN3-3′D4 was recovered in C6/36 cells and Vero cells, whilerDEN3-3′D4Δ30 could only be recovered in Vero cells. Mutant viruses werethen passaged once in Vero cells followed by biological cloning by twoterminal dilutions in Vero cells. rDEN3-3″D4 and rDEN3-3′D4Δ30 were thenpassaged four or six times in Vero cells, respectively. The geneticsequence of the NS5-3′-UTR junction and 3′-UTR was found to be correctfor rDEN3-3′D4 and rDEN3-3′D4Δ30. Therefore, both viruses were studiedfurther.

Mutations were also identified in the rDEN3-3′D4Δ30 virus compared tothe DEN3 p3 plasmid cDNA clone (5-UTR and genes) and DEN4 p4 cDNA clone(3′-UTR) (Table 5).

TABLE 5 Mutations in the rDEN3-3D4A30 virus compared to the DEN3 p3plasmid cDNA clone (5′-UTR and genes) and DEN4 p4 cDNA clone (3′-UTR)Nucleotide Nucleotide Amino acid Amino acid Virus Gene positionsubstitution position change rDEN3-3′D4A30 C   250 U → C  52 silent NS3 5899 U → C 462 silent NS4B^(a)  7164 U → C 115 Val → Ala 3′-UTR 10534A → G — — ^(a)The 7164 mutation is a Vero cell adaptation mutation whichwas engineered into the cDNA construct.

Replication of DEN3 Mutant Viruses in SCID-HuH-7 Mice

The four deletion mutant viruses (rDEN3Δ30/31, rDEN3Δ61, rDEN3Δ80, andrDEN3Δ86) which were found to replicate to high titer in Vero cells andwere confirmed to have the correct 3′-UTR sequence and the rDEN3-3′D4and rDEN3-3′D4Δ30 viruses were first evaluated in SCID-HuH-7 mice. TherDEN3-3′D4 and rDEN3-3′D4Δ30 were compared to determine the effect onreplication of the 3′-UTR chimerization and any further attenuationconferred by the Δ30 mutation. SCID-HuH-7 mice contain solid tumors ofthe HuH-7 human hepatoma cell line, and analysis of virus replication inthis mouse model serves as a surrogate for DEN virus replication in thehuman liver. Numerous DEN virus mutant viruses have been identified byevaluation in SCID-HuH-7 mice (Blaney J E, et al. 2002 Virology300:125-139; Hanley et al. 2004 Vaccine 22:3440-3448; Blaney J E et al.2006 Viral Immunol. 19:10-32). This mouse model provided the originalevidence that the rDEN3Δ30 virus was not attenuated compared to parentvirus rDEN3, while the antigenic chimeric virus, rDEN3/4Δ30, wasapproximately 100-fold restricted in replication in the SCID-HuH-7 micewhen compared to wild type parent viruses (Blaney J E et al. 2004 Am JTrop Med Hyg 71:811-821).

For analysis of virus replication in SCID-HuH-7 mice, four to sixweek-old SCID mice (Tac:Icr:Ha(ICR)-Prkdc^(scid)) (Taconic Farms) wereinjected intraperitoneally with 0.1 mL phosphate-buffered salinecontaining 10⁷ HuH-7 cells which had been propagated in tissue culture.Tumors were detected in the peritoneum five to six weeks aftertransplantation, and tumor-bearing mice were infected by directinoculation into the tumor with 10⁴ PFU of virus in 50 μl Opti-MEM I.Serum was collected from infected mice on day 7 post-infection andfrozen at −80° C. The virus titer was determined by plaque assay in Verocells.

As indicated in Table 6, wild type DEN3 Sleman/78 replicated to a meanpeak virus titer of nearly 10^(6.9) PFU/ml. Although a decreased levelof replication was observed for each of the six mutant viruses, thedifferences in replication were not statistically significant. However,rDEN3Δ86 and rDEN3-3′D4Δ30 were more than 10-fold restricted inreplication compared to wild type DEN3 virus, while the replication ofrDEN3Δ30/31 was slightly less than 10-fold restricted. On the basis ofthis arbitrary cut-off, these three viruses were selected for furtherevaluation. It is important to note that the rDEN4Δ30 virus which has awell-characterized, attenuation and non-reactogenic phenotype in humanswas found to be only 6-fold restricted in replication in SCID-HuH-7 micecompared to wild type rDEN4 virus (Hanley et al. 2004 Vaccine22:3440-3448).

TABLE 6 Replication of mutant DEN3 viruses in HuH-7-SCID mice. Mean peakFold-reduction No. of virus titer compared to Virus¹ mice (log₁₀pfu/ml ±SE) DEN3 (Sleman/78) DEN3 (Sleman/78) 8 6.9 ± 0.1 — rDEN3Δ30/31 8 6.0 ±0.3 8 rDEN3Δ61 9 6.3 ± 0.2 4 rDEN3Δ80 9 6.3 ± 0.3 4 rDEN3Δ86 10 5.6 ±0.4 20 rDEN3-3′D4 11 6.5 ± 0.4 3 rDEN3-3′D4Δ30 9 5.7 ± 0.2 16 ¹Groups ofHuH-7-SCID mice were inoculated into the tumor with 4.0 log₁₀ PFU of theindicated virus. Serum was collected on day 7 and virus titer wasdetermined in Vero cells.

Because the rDEN3-3′D4Δ30 virus and the rDEN3Δ30/31 and rDEN3Δ86 virusesencode the full set of DEN3 structural and non-structural proteins, theywould be expected to induce the full complement of humoral and cellularimmunity. This more complete immune induction would be advantageouscompared to that induced by the chimeric rDEN3/4Δ30, which encodes onlythe structural proteins of DEN3.

Replication of DEN3 Mutant Viruses in Tissue Culture

The level of virus replication in Vero cells and mosquito C6/36 cellswas assessed for the rDEN3Δ30/31 and rDEN3Δ86 deletion mutant virusesand the rDEN3-3′D4 viruses with and without Δ30. Replication in Verocells was analyzed because these cells are the substrate formanufacture, while growth in C6/36 cells was assessed becauseattenuation phenotypes in these mosquito cells may be associated withrestricted replication in Aedes mosquitoes which serve as the vector forDEN virus transmission (Hanley et al. 2003 Virology 312:222-232).

Growth kinetics were evaluated as follows. Confluent monolayers of Verocells and C6/36 cells in 75 cm² flasks were infected at a multiplicityof infection of 0.01. Aliquots of 0.5 ml tissue culture supernatant wereremoved daily for seven days, combined with SPG stabilizer, and frozenat −80° C. Virus titer of all samples was determined by plaque assay inVero cells. The limit of detection for the plaque assay is 1.0log₁₀PFU/ml.

The replication kinetics of each virus in both cell lines is shown inFIG. 19. In Vero cells, rDEN3Δ30/31, rDEN3Δ86, and rDEN3-3′D4Δ30replicated to a peak level that approximated that of wild type rDEN3 andwith similar kinetics to that of wild type rDEN3. These three vaccinecomponents reached peak virus titers of 6.5 to 6.7 log₁₀PFU/ml whichdemonstrates the feasibility of manufacture for each of these viruses.In Vero cells, the rDEN3-3′D4 virus replicated to a peak titer of 7.8log₁₀PFU/ml which is nearly 100-fold higher than that observed for wildtype rDEN3 indicating that inclusion of the DEN4 3′-UTR may augmentreplication in Vero cells. This could also be attributed to moreefficient Vero cell adaptation of the rDEN3-3′D4 virus. rDEN4 replicatesto a peak titer of approximately 8.0 log₁₀PFU/ml which indicates thatthe chimeric virus achieves a peak titer that does not exceed that ofeither of its parent viruses (Blaney J E et al. 2006 Viral Immunol.19:10-32).

Analysis of virus replication in C6/36 cells demonstrated that rDEN3Δ86and rDEN3-3′D4Δ30 reached peak titers approximately 10-fold lower thanthe peak virus titer of wild type rDEN3 virus, 6.9 log₁₀ PFU/ml (FIG.19). The rDEN3-3′D4 virus replicated to a peak titer similar to thatobserved for wild type rDEN3. The most striking result was the lack ofreplication observed in C6/36 cells for the rDEN3Δ30/31 virus. After day1, virus was not detected in culture medium from C6/36 cells infectedwith rDEN3Δ30/31 virus despite the efficient replication observed inVero cells. These results were confirmed in a second independent growthcurve experiment and indicate a host range attenuation phenotype intissue culture which is envisioned as being accompanied by anattenuation phenotype in mosquitoes as well.

Replication and Immunogenicity of DEN3 Mutant Viruses in Rhesus Monkeys

Based on the slight attenuation in SCID-HuH-7 mice and efficient growthin Vero cells, rDEN3Δ30/31, rDEN3Δ86, and rDEN3-3′D4Δ30 were evaluatedin rhesus monkeys. The mutant viruses were compared with wild type DEN3for level and duration of viremia, neutralizing antibody induction, andthe ability to confer protection from wild type DEN3 virus challenge.The rDEN3-3′D4 virus was also evaluated to discern the contribution ofthe 3′-UTR chimerization upon attenuation with and without the Δ30mutation. An attenuation phenotype in rhesus monkeys has generally beena strong predictor of safety for vaccine components in clinical trialsincluding rDEN4Δ30, rDEN1Δ30, and rDEN2/4430 (Blaney J E et al. 2006Viral Immunol. 19:10-32).

Groups of four rhesus monkeys were inoculated subcutaneously with 10⁵PFU of the indicated viruses (Table 7). Two monkeys were mock infectedwith virus diluent. For detection of viremia, serum was collected ondays 0-8 and on day 10 and frozen at −80° C. Virus titer in serumsamples was determined by plaque assay in Vero cells. Serum wascollected on day 28 for detection of neutralizing antibodies directedagainst DEN3. Levels of neutralizing antibodies were determined using aplaque reduction neutralization assay in Vero cells against wild typeDEN3 virus. On day 35 post-infection, all monkeys were challenged bysubcutaneous infection with 10⁵ PFU DEN3 wild type virus. Serum wascollected on days 0-8 and on day 10 and frozen at −80° C. Virus titer inserum samples was determined by plaque assay in Vero cells.

TABLE 7 Replication and immunogenicity of rDEN3 mutant viruses in rhesusmonkeys. Geometric mean serum Post-challenge⁴ % of Mean no. of Mean peakneutralizing antibody % of Mean peak monkeys viremic virus titer² titermonkeys virus titer² No. of with days (log₁₀pfu/ml ± (reciprocaldilution)³ with (log₁₀ pfu/ml ± Virus¹ monkeys viremia per monkey SE)Day 0 Day 28 viremia SE) DEN3 (Sleman/78) 4 100 3.5 1.8 ± 0.1 <5 253 0<1.0 rDEN3Δ30/31 4 0 0 <1.0 <5 304 0 <1.0 rDEN3Δ86 4 0 0 <1.0 <5 224 0<1.0 rDEN3-3’D4 4 75 1.5 1.3 ± 0.2 <5 229 0 <1.0 rDEN3-3’D4Δ30 4 0 0<1.0 <5 77 0 <1.0 mock infected 2 0 0 <1.0 <5 <5 100 1.8 ± 0.2 ¹Groupsof rhesus monkeys were inoculated subcutaneously on day 0 with 5.0 log₁₀PFU of the indicated virus in a 1 ml dose. Serum was collected daily ondays 0-8 and 10 and once on day 28. ²Virus titer in serum was determinedby plaque assay in Vero cells. ³Plaque reduction (60%) neutralizingantibody titers were determined using DEN3 (Sleman/78). ⁴Monkeys werechallenged after 35 days with DEN3 (Sleman/78) administeredsubcutaneously in a 1 ml dose containing 5.0 log₁₀ PFU. Serum wascollected daily on days 0-8 and 10.

Wild type DEN3 Sleman/78 virus replicated in rhesus monkeys to a meanpeak virus titer of 1.8 log₁₀PFU/ml serum with all monkeys developingviremia (Table 7). These results parallel previous studies of DEN3 inrhesus monkeys (Blaney J E et al. 2004 Am J Trop Med Hyg 71:811-821). Noviremia was detected in any monkey infected with any of the threevaccine components, rDEN3Δ30/31, rDEN3Δ86, or rDEN3-3′D4Δ30demonstrating a clear attenuation phenotype for each of these viruses inrhesus monkeys. Interestingly, the rDEN3-3′D4 virus was detected in 75%of monkeys with a mean peak virus titer of 1.3 log₁₀PFU/ml serumsuggesting that the presence of the Δ30 mutation is critical forattenuation of the 3′-UTR chimeric virus. Despite the lack of detectableviremia, mean neutralizing antibody levels in monkeys infected withrDEN3Δ30/31 and rDEN3Δ86 reached levels similar to that of wild typeDEN3 virus, 1:253 (Table 7). In contrast, the rDEN3-3′D4Δ30 virusinduced mean neutralizing antibody levels approximately three-fold lowerthan DEN3. However, 100% of monkeys immunized with each vaccinecomponent seroconverted as defined by a four-fold or greater rise inserum neutralizing antibody levels after infection. Thus all monkeyswere deemed to be infected by each of the vaccine components despite thelack of detectable viremia. Determination of virus titer in serum afterchallenge with DEN3 virus indicated that immunization with each of thevaccine components induced complete protection from detectable viremiaas would be expected given the observed neutralizing antibody levels.

Replication in Mosquitoes

Replication of rDEN3 and rDEN3Δ30/31 was studied in Toxorynchitesamboinenesis mosquitoes. Intrathoracic inoculation of serial ten-folddilutions of test virus was performed as described previously (Troyer J.M. e al. 2001 Am. J. Trop. Med. Hyg. 65:414-9). After a 14 dayincubation, heads were separated and homogenized in diluent. Virus titerin head homogenates was determined by plaque assay in Vero cells.

Based on the attenuation of rDEN3Δ30/31 in rhesus monkeys and itsrestricted replication in C6/36 mosquito cells, rDENΔ30/31 was comparedto wild type rDEN3 for infectivity and level of replication in highlysensitive Toxorynchites amboinensis mosquitoes (Table 8). Ten-foldserial dilutions of virus were inoculated intrathoracically, and theability to infect head tissues was evaluated by performing a plaqueassay on mosquito head homogenates after a 14 day incubation. Theinfectivity of rDEN3 and rDENΔ30/31 was very similar as the 50% mosquitoinfectious dose was approximately 10^(1.3) PFU for both viruses (Table8). However, the level of replication of rDENΔ30/31 in the heads ofinfected mosquitoes was about 5- to 50-fold reduced. This reduction wassignificant at the 10^(2.3) and 10^(1.3) PFU doses tested. This findingindicates that although rDENΔ30/31 has infectivity for Toxorynchites byintrathoracic infection similar to that of wild type rDEN3, there is astatistically significant restriction in the level of replication inmosquitoes afforded by the Δ30/31 mutation.

TABLE 8 Replication of rDEN3 and rDEN3Δ30/31 in Toxorynchitesamboinensis Mean virus Reduction (log₁₀) Dose^(a) No % titer^(c)compared to same Virus (log₁₀PFU) tested infected^(b) (log₁₀PFU/head)dose of wt virus rDEN3 wt 2.3 20 90 4.2 ± 0.1^(d) 1.3 19 53 4.2 ±0.1^(e) 0.3 17 18 4.3 ± 0.3 rDEN3Δ30/31 2.3 12 83 2.7 ± 0.3^(d) 1.5 1.316 44 3.1 ± 0.3^(e) 1.1 0.3 8 13 3.6 ± 0.0 0.7 ^(a)Virus titeradministered intrathoracically in a 0.2 μl inoculum. ^(b)Percentage ofmosquitoes with detectable virus at day 14 post-inoculation wasdetermined by plaque assay on mosquito head homogenates in Vero cells.^(c)Calculated using only values of virus-positive heads. ^(d)For10^(2.3) PFU dose of rDEN3 and rDEN3Δ30/31, mean virus titers weresignificantly different as determined by a Tukey-Kramer post-hoc test (P< 0.001). ^(e)For 10^(1.3) PFU dose of rDEN3 and rDEN3Δ30/31, mean virustiters were significantly different as determined by a Tukey-Kramerpost-hoc test (P < 0.005).

While the present invention has been described in some detail forpurposes of clarity and understanding, one skilled in the art willappreciate that various changes in form and detail can be made withoutdeparting from the true scope of the invention. All figures, tables, andappendices, as well as patents, applications, and publications, referredto above, are hereby incorporated by reference.

1. A nucleic acid encoding a dengue virus or chimeric dengue viruscomprising a mutation in the 3′untranslated region (3′-UTR) selectedfrom the group consisting of: (a) a Δ30 mutation that removes the TL-2homologous structure in each of the dengue virus serotypes 1, 2, 3, and4, and nucleotides additional to the Δ30 mutation deleted from the3′-UTR that removes sequence in the 5′ direction as far as the 5′boundary of the TL-3 homologous structure in each of the dengue virusserotypes 1, 2, 3, and 4; and (b) a replacement of the 3′-UTR of adengue virus of a first serotype with the 3′-UTR of a dengue virus of asecond serotype, optionally containing the Δ30 mutation and nucleotidesadditional to the Δ30 mutation deleted from the 3′-UTR.
 2. The nucleicacid encoding a dengue virus or chimeric dengue virus of claim 1 whereinthe mutation is (a).
 3. The nucleic acid encoding a dengue virus orchimeric dengue virus of claim 2 wherein the mutation removes the TL-2homologous structure and removes sequence up to and including the TL-3homologous structure in a contiguous manner contiguous to the Δ30mutation.
 4. The nucleic acid encoding a dengue virus or chimeric denguevirus of claim 3 wherein the mutation is the Δ86 mutation, such that theΔ86 mutation deletes nucleotides from about 228 to about 145 of DEN1,nucleotides from about 228 to about 144 of DEN 2, nucleotides from about228 to about 143 of DEN3, and nucleotides from about 228 to about 143 ofDEN4, designated with the reverse-direction numbering system.
 5. Thenucleic acid encoding a dengue virus or chimeric dengue virus of claim 4wherein the serotype is DEN3.
 6. The nucleic acid encoding a denguevirus or chimeric dengue virus of claim 2 wherein the mutation removesboth the TL-2 homologous structure and the TL-3 homologous structure ina noncontiguous manner noncontiguous to the Δ30 mutation.
 7. The nucleicacid encoding a dengue virus or chimeric dengue virus of claim 6 whereinthe mutation is the Δ30 131 mutation, such that the Δ30 mutation deletesnucleotides from about 174 to about 145 of DEN 1, nucleotides from about173 to about 144 of DEN 2, nt nucleotides from about 173 to about 143 ofDEN3, and nucleotides from about 172 to about 143 of DEN4, designatedwith the reverse-order numbering system, and the Δ31 mutation deletesnucleotides from about 258 to about 228 of DEN1, nucleotides from about258 to about 228 of DEN 2, nucleotides from about 258 to about 228 ofDEN3, and nucleotides from about 258 to about 228 of DEN4, designatedwith the reverse-order numbering system.
 8. The nucleic acid encoding adengue virus or chimeric dengue virus of claim 7 wherein the serotype isDEN3.
 9. The nucleic acid encoding a dengue virus or chimeric denguevirus of claim 1 wherein the mutation is (b).
 10. The nucleic acidencoding a dengue virus or chimeric dengue virus of claim 9 wherein the3′-UTR of DEN1 is replaced with the 3′-UTR of dengue virus serotypes 2,3, or 4, the 3′-UTR of DEN2 is replaced with the 3′-UTR of dengue virusserotypes 1, 3, or 4, the 3′-UTR of DEN3 is replaced with the 3′-UTR ofdengue virus serotypes 1, 2, or 4, or the 3′-UTR of DEN4 is replacedwith the 3′-UTR of dengue virus serotypes 1, 2, or
 3. 11. The nucleicacid encoding a dengue virus or chimeric dengue virus of claim 10further comprising the Δ30 mutation.
 12. The nucleic acid encoding adengue virus or chimeric dengue virus claim 10 further comprising theΔ30 mutation and nucleotides additional to the Δ30 mutation deleted fromthe 3′-UTR.
 13. The nucleic acid encoding a dengue virus or chimericdengue virus of claim 9 wherein the 3′-UTR of DEN3 is replaced with the3′-UTR of dengue virus serotypes 1, 2, or
 4. 14. The nucleic acidencoding a dengue virus or chimeric dengue virus of claim 13 furthercomprising the Δ30 mutation.
 15. The nucleic acid encoding a denguevirus or chimeric dengue virus of claim 13 further comprising the Δ30mutation and nucleotides additional to the Δ30 mutation deleted from the3′-UTR.
 16. The nucleic acid encoding a dengue virus or chimeric denguevirus of claim 9 selected from the group consisting of: a) rDEN1-3′D2,rDEN1-3′D2x, rDEN1-3′D3, rDEN1-3′D3x, rDEN1-3′D4, rDEN1-3′D4x;rDEN1/2-3′D1, rDEN1/2-3′D1x, rDEN1/2-3′D3, rDEN1/2-3′D3x, rDEN1/2-3′D4,rDEN1/2-3′D4x; rDEN1/3-3′D1, rDEN1/3-3′D1x, rDEN1/3-3′D2, rDEN1/3-3′D2x,rDEN1/3-3′D4, rDEN1/3-3′D4x; rDEN1/4-3′D1, rDEN1/4-3′D1x, rDEN1/4-3′D2,rDEN1/4-3′D2x, rDEN1/4-3′D3, rDEN1/4-3′D3x; b) rDEN2-3′D1, rDEN2-3′D1x,rDEN2-3′D3, rDEN2-3′D3x, rDEN2-3′D4, rDEN2-3′D4x; rDEN2/1-3′D2,rDEN2/1-3′D2x, rDEN2/1-3′D3, rDEN2/1-3′D3x, rDEN2/1-3′D4, rDEN2/1-3′D4x;rDEN2/3-3′D1, rDEN2/3-3′D1x, rDEN2/3-3′D2, rDEN2/3-3′D2x, rDEN2/3-3′D4,rDEN2/3-3′D4x; rDEN2/4-3′D1, rDEN2/4-3′D1x, rDEN2/4-3′D2, rDEN2/4-3′D2x,rDEN2/4-3′D3, rDEN2/4-3′D3x; c) rDEN3-3′D1, rDEN3-3′D1x, rDEN3-3′D2,rDEN3-3′D2x, rDEN3-3′D4, rDEN3-3′D4x; rDEN3/1-3′D2, rDEN3/1-3′D2x,rDEN3/1-3′D3, rDEN3/1-3′D3x, rDEN3/1-3′D4, rDEN3/1-3′D4x; rDEN3/2-3′D1,rDEN3/2-3′D1x, rDEN3/2-3′D3, rDEN3/2-3′D3x, rDEN3/2-3′D4, rDEN3/2-3′D4x;rDEN3/4-3′D1, rDEN3/4-3′D1x, rDEN3/4-3′D2, rDEN3/4-3′D2x, rDEN3/4-3′D3,rDEN3/4-3′D3x; and d) rDEN4-3′D1, rDEN4-3′D1x, rDEN4-3′D2, rDEN4-3′D2x,rDEN4-3′D3, rDEN4-3′D3x; rDEN4/1-3′D2, rDEN4/1-3′D2x, rDEN4/1-3′D3,rDEN4/1-3′D3x, rDEN4/1-3′D4, rDEN4/1-3′D4x; rDEN4/2-3′D1, rDEN4/2-3′D1x,rDEN4/2-3′D3, rDEN4/2-3′D3x, rDEN4/2-3′D4, rDEN4/2-3′D4x; rDEN4/3-3′D1,rDEN4/3-3′D1x, rDEN4/3-3′D2, rDEN4/3-3′D2x, rDEN4/3-3′D4, rDEN4/3-3′D4x;where x is a mutation listed in Table
 2. 17. An immunogenic compositioncomprising a nucleic acid encoding a dengue virus or chimeric denguevirus according to claim 1 or a dengue virus or chimeric dengue viruscomprising said nucleic acid.
 18. The immunogenic composition of claim17 that is tetravalent for dengue serotypes 1, 2, 3, and
 4. 19. A methodof inducing an immune response to a dengue virus in a patient comprisingadministering the immunogenic composition of claim 17 to a patient toinduce an immune response to a dengue virus.
 20. A method of producing anucleic acid encoding a dengue virus or chimeric dengue virus comprisingintroducing a mutation into the 3′ untranslated region (3′-UTR) selectedfrom the group consisting of: (a) a Δ30 mutation that removes the TL-2homologous structure in each of the dengue virus serotypes 1, 2, 3, and4, and nucleotides additional to the Δ30 mutation deleted from the3′-UTR that removes sequence in the 5′ direction as far as the 5′boundary of the TL-3 homologous structure in each of the dengue virusserotypes 1, 2, 3, and 4; and (b) a replacement of the 3′-UTR of adengue virus of a first serotype with the 3′-UTR of a dengue virus of asecond serotype, optionally containing the Δ30 mutation and nucleotidesadditional to the Δ30 mutation deleted from the 3′-UTR.